The distribution of subterranean copepods may reflect the persistence of cave assemblages in relation to the environmental health of the overlying landscape. Areas supporting groundwater fauna were established by modelling the persistence of seven copepod species using a geographical information system (GIS). Environmental drivers were found to influence subterranean copepod distribution in the caves of the Romanian Carpathians. Habitat-based modelling, using ordinary least squares regression and geographically-weighted regression to identify the significant predictors explaining copepod habitat suitability, predicted suitable areas for the selected taxa. The most constant predictor was land cover, a measure of human impact and climate change, followed by precipitation and altitude. The model performed well for the majority of analysed taxa, and the areas predicted as suitable for narrowly distributed taxa overlapped with observed distributions. GIS facilitated the prediction of suitable habitat, and also enabled spatial autocorrelation to be tested. The results of this study demonstrate the importance of sustainable management of the terrestrial surface in limestone areas in conserving copepod biodiversity.